Venky's chairperson Anuradha Desai insists the Red Devils contacted the defender before being authorised to do so, while the Premier League champions maintain their innocence
The young defender recently sealed a deal worth £20.5 million with add-ons, and switched his allegiance to the Old Trafford outfit.
Now Rovers' owner, Venky's chairperson Anuradha Desai, has hit out at the Red Devils, insisting that her club could have lodged an official complaint to the Premier League.
But after holding talks with manager Steve Kean, Rovers decided that it would have been unfair if the struggle that could potentially have ensued had impacted on the 19-year-old's career.
"We have reasons to believe that the player's agent and maybe the player had been in touch [with United] for two to three months before permission was granted," Desai told The Mail on Sunday.
"I was ready to take Manchester United on, ready to go to a tribunal if that's what it led to. But we spoke at length to Steve Kean and we knew Phil wanted to go to United.
"We concluded that the person who would be most damaged by a delay and legal action was Phil. That wasn't fair on him. There was a release clause for £16.5m and the total deal was £4m more with the add-ons. We wish Phil well.
"Phil is an outstanding young English player and I'm proud of the role Blackburn played in developing him. We made him an enormous offer to stay with us and we wanted to keep him."
For their part, United have denied the allegations made by Blackburn, as a spokesperson for the Red Devils said: "We had the appropriate permissions to speak to Phil Jones."
Jones' agent, John Colquhoun, added: "I won't be commenting on the confidential process that was undertaken.
"Everyone is telling me they're happy with what went on so, unless I hear different and unless I've got questions to answer, I don't feel I have to comment."